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Understanding humanity's shared history means understanding what happened in Africa. But figuring out what happened in Africa has been a difficult task. Not every area is well represented in the fossil history, and most African environments aren't conducive to the preservation of ancient DNA. DNA sequencing of modern African populations lags behind other regions, in part because DNA sequencing hardware is more common elsewhere. Finally, as in many other areas, massive migrations within the continent have helped scramble the genetic legacy of the past.

Now, researchers are describing a new window into our collective past: DNA from ancient skeletons found in a rock shelter in West Africa. The skeletons come from a location and time that are both near the origin of the Bantu expansion that spread West African peoples across the entirety of Africa but have little in common with Bantu-speaking populations. Yet, at the same time, they provide hints of what might have happened very early in humanity's history, including the existence of a lineage of archaic humans we've not yet identified.

Right time, right place

The skeletons come from a site called Shum Laka, which is located in a grassland area of Cameroon. For those not up on their African geography, Cameroon is located at the angle where West Africa meets Southern Africa. This is also the region where the Bantu people put together a collection of agricultural and metallurgical technologies that allowed them to sweep across the rest of the continent, leaving their linguistic and genetic mark on many other populations.

Further Reading

Artifacts indicate that humans have occupied Shum Laka on and off for at least 30,000 years, and there are skeletons that date back thousands of years. The research team behind the new work tried to obtain DNA from 18 different skeletons and succeeded with four: a young child and an adolescent from a single grave 8,000 years old, and neighboring graves of two young boys from about 3,000 years ago. The latter date is roughly similar to that of the start of the Bantu expansion, suggesting these skeletons could tell us about the origin of these people.

Analysis of the DNA sequences indicates that each skeleton was closely related to the one buried with it, with a degree of genetic similarity that you'd see in half-siblings. The mitochondrial genome, which is inherited from an individual's mother, weren't especially informative, as they match variants that are found widely in Africa. The same is true for one of the Y chromosomes. But another Y is a rare version that's only found in a few modern populations in Africa and seems to have been introduced into modern humans by interbreeding with an archaic human, much like the DNA introduced to Eurasians from Neanderthals. The version from the skeleton is a new branch of this old lineage and appears to have originated over 20,000 years ago.

But comparisons of the skeletons' DNA with modern Bantu-speakers showed that the two weren't very closely related. And comparisons with other people from that region of Africa indicate that their recent shared ancestry is rather small. Instead, the skeletons are most closely related to modern groups of hunter-gatherers from Central Africa. Thus, the hope that they were associated with the origin of Bantu speakers doesn't seem to have panned out.

Rebuilding the past

But if the skeletons don't shed light on the Bantu, they may provide new insight into humanity as a whole. Previous analyses suggested that the earliest branch of modern humans ended up forming populations of hunter-gatherers presently found in southern Africa. With the analysis redone using these new genomes, the hunter-gatherer groups from Central Africa now seem to have split off at roughly the same time, and may be even older. This suggests a general expansion of modern humans within Africa shortly after their origin, about 250,000 years ago.

The new data also suggests that modern humans contain a "ghost lineage," meaning a group for which we have no physical evidence. The data from these genomes, combined with some additional modern samples from West Africa, suggest that an unknown group contributed to hunter-gatherers from both East and West Africa. But it doesn't appear to have persisted to the present as a distinct population.

All of this reinforces the idea that there's been a complicated mix of things happening within Africa, with multiple groups being isolated from each other for extended periods and then intermingling in limited ways. Somewhere in all of that, one population branched off and occupied much of the rest of the world. And we now have evidence of at least two "ghost lineages" in humanity's past. One appears to have been present early in the history of the Neanderthals and Denisovans and is hinted at by its DNA. The other appears to have contributed to African populations but not survived to the present.

While this represents an interesting advance in our understanding of humanity's collective history, we've still got a long way to go before we have a diverse sample of genomes from African populations. And, until we fill in the picture more completely, the chance for further surprises is quite high.

63 Reader Comments

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

The Sahara alternates between being a desert and a savannah on the scale of thousands of years. It was quite habitable not so long ago, just prior to the Pharaonic civilization.

The biggest effect is a lack of scale of recognizable things, which is behind the idea of miniature faking. Miniature photography replicating real images is broke with any kind of real life item to provide scale. The lack of depth of field is easy to do by having a narrow aperture. Wider ones tend to blur everything except that which is in focus.

I'm guessing they had plenty of light, or it was a tripod shot over a long period of time with a relatively high F-stop to shoot that image.

Sorry, I did photography on a semi-professional level and know a lot of photographic tricks.

If one looks closely at that, those furnishings are tables, not benches. That provides a good scale for how large the dig is, if one assumes they're about waist high on most people (typically 28"-30"). The wood appears to be 1" planking, stacked up over the edge of the dig so people don't stumble into it or damage the top of the hole's sides.

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

The Sahara alternates between being a desert and a savannah on the scale of thousands of years. It was quite habitable not so long ago, just prior to the Pharaonic civilization.

...until a tsunami hit the North African coast around CE 365, devastating much of the crop lands through seawater and causing thousands of deaths in the (then) roman population.

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

The Sahara alternates between being a desert and a savannah on the scale of thousands of years. It was quite habitable not so long ago, just prior to the Pharaonic civilization.

...until a tsunami hit the North African coast around CE 365, devastating much of the crop lands through seawater and causing thousands of deaths in the (then) roman population.

That's not the Sahara, that's the Mediterranean coastal region, which is a couple of hundred kilometers wide at most. The Sahara starts further inland, and had already been full desert for several thousand years by that time.

"North Africa was nearly completely vegetated during the height of the AHP (Jolly et al., 1998) and populated with nomadic hunter-gatherer communities that increasingly practiced pastoralism (husbandry of cattle, sheep, and goats; Hoelzmann et al., 2002; Kuper and Kröpelin, 2006). The rock art images in Figure 1 depict impressions of this life. Towards the end of the African Humid Period between 7,000 and 5,000 years ago the progressive desiccation of the region led to a widespread depopulation and abandonment of North African sites. These populations did not disappear, however. The large-scale exodus was coincident with the rise of sedentary life and pharaonic culture along the Nile River (a perennial water source) and the spread of pastoralism throughout the continent (Kuper and Kröpelin, 2006)."

"North Africa was nearly completely vegetated during the height of the AHP (Jolly et al., 1998) and populated with nomadic hunter-gatherer communities that increasingly practiced pastoralism (husbandry of cattle, sheep, and goats; Hoelzmann et al., 2002; Kuper and Kröpelin, 2006). The rock art images in Figure 1 depict impressions of this life. Towards the end of the African Humid Period between 7,000 and 5,000 years ago the progressive desiccation of the region led to a widespread depopulation and abandonment of North African sites. These populations did not disappear, however. The large-scale exodus was coincident with the rise of sedentary life and pharaonic culture along the Nile River (a perennial water source) and the spread of pastoralism throughout the continent (Kuper and Kröpelin, 2006)."

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

Perhaps the very low population density of Africa made meeting other groups and intermingling less likely?

Even today the 54 countries on the African continent (30 million square kilometres) have fewer inhabitants than just China (9 million sq. km), let alone thousands of years ago.

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

Geography and climate probably. Hunter gatherers often follow the migration patterns of their prey. For example, they might go up and down the mountains between wet and dry season, much like modern day pastoralists often do. They also depend on natural resources such as flint to be nearby.

So even if two human populations are not separated by an impassible barrier, they might simply never intersect, because they will never venture too far away from the places they absolutely need for survival.

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

Perhaps the very low population density of Africa made meeting other groups and intermingling less likely?

Even today the 54 countries on the African continent (30 million square kilometres) have fewer inhabitants than just China (9 million sq. km), let alone thousands of years ago.

An aid worker I used to know said that Africa's problem is not overpopulation but underpopulation. Many areas just don't have enough people to run a developed society with access to electricity, medicine, pesticides and fertilisers.It goes against the overpopulation narrative, but from a climate change point of view overpopulation is a US and European issue since each one of us is equivalent in carbon resource terms to maybe ten or more average Africans.

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

Perhaps the very low population density of Africa made meeting other groups and intermingling less likely?

Even today the 54 countries on the African continent (30 million square kilometres) have fewer inhabitants than just China (9 million sq. km), let alone thousands of years ago.

An aid worker I used to know said that Africa's problem is not overpopulation but underpopulation. Many areas just don't have enough people to run a developed society with access to electricity, medicine, pesticides and fertilisers.It goes against the overpopulation narrative, but from a climate change point of view overpopulation is a US and European issue since each one of us is equivalent in carbon resource terms to maybe ten or more average Africans.

I can see that, to some extent. Although I don’t know if that still works today. African countries tend to be highly urbanised with the majority of Africans now living in big cities. They have cities with more inhabitants than many countries. Visit Lagos and suddenly LA has a quaint village feeling to it.

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

Perhaps the very low population density of Africa made meeting other groups and intermingling less likely?

Even today the 54 countries on the African continent (30 million square kilometres) have fewer inhabitants than just China (9 million sq. km), let alone thousands of years ago.

In the era of hunter gathering, everywhere had low population density. The issue is that the skills needed to survive in rainforests of the Cameroon, the plains of Serengeti and the Kalahari desert are very different. Africa is a huge continent with many different environments. As mentioned above Lagos is a mega city with a population of 30 million and Nigeria has a population of 200 million at 4 times the population density of the USA.

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

Perhaps the very low population density of Africa made meeting other groups and intermingling less likely?

Even today the 54 countries on the African continent (30 million square kilometres) have fewer inhabitants than just China (9 million sq. km), let alone thousands of years ago.

An aid worker I used to know said that Africa's problem is not overpopulation but underpopulation. Many areas just don't have enough people to run a developed society with access to electricity, medicine, pesticides and fertilisers.It goes against the overpopulation narrative, but from a climate change point of view overpopulation is a US and European issue since each one of us is equivalent in carbon resource terms to maybe ten or more average Africans.

I don't buy that. Iceland has a very tiny population on a large landmass and still manage operate very well. Just 350 000 people and very remote. Yet they have their own airline, power stations, post office, advance health care etc. Australia and Canada also cover wast land areas without having very high population.

It is primarily a question of development. Iceland is far more developed in every sense: education of population, sophistication of institutions, industry and income level. Increasing the population does not solve the fundamental problem which is poverty. A lot of India despite dense population is no better of.

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

Perhaps the very low population density of Africa made meeting other groups and intermingling less likely?

Even today the 54 countries on the African continent (30 million square kilometres) have fewer inhabitants than just China (9 million sq. km), let alone thousands of years ago.

An aid worker I used to know said that Africa's problem is not overpopulation but underpopulation. Many areas just don't have enough people to run a developed society with access to electricity, medicine, pesticides and fertilisers.It goes against the overpopulation narrative, but from a climate change point of view overpopulation is a US and European issue since each one of us is equivalent in carbon resource terms to maybe ten or more average Africans.

I don't buy that. Iceland has a very tiny population on a large landmass and still manage operate very well. Just 350 000 people and very remote. Yet they have their own airline, power stations, post office, advance health care etc. Australia and Canada also cover wast land areas without having very high population.

It is primarily a question of development. Iceland is far more developed in every sense: education of population, sophistication of institutions, industry and income level. Increasing the population does not solve the fundamental problem which is poverty. A lot of India despite dense population is no better of.

One factor that often gets forgotten is the constant resource and talent drain that Africa has been going through since the 1500's. Up until the abolishment of slavey, the healthiest and fittest portions of the population where shipped overseas. and by the time it had fully ended by the early 1900's you then still had a talent drain where young talented africans till this where leaving Africa in order to seek "higher education and expertise" to bring back home only thing is after they recieve the education they came to get, they tend to settle down in those respctive countries and not go back. Again this leaves the african dispora in a worsening position as time goes on. Talent that would help in building all the relevant infrastructure, instutituions, and industry just inst ther in the quaties needed. Lastly, the exploitation of africa's resources is well known at this point. Whether its blood diamonds of west africa or the cobalt/silicon mining exploitation in congo, the rest of the world mainly the west as of until recently has been draining the riches out of africa.

P.S fun fact on the whole population thing. According to UN reports, by 2050 there will be 3.6 Billion poeple in afirca alone making it the worlds most populated continent.

Africa is pretty damn big and the Sahara desert which formed 7 million years ago a pretty big barrier to leaving Africa. That explains a lot about why we have several migrations out of Africa. What explains multiple populations in the rest of Africa getting isolated for a while then getting back in touch again?

Just distance and slow movement rates? Different geographies and climates?

Africa is oriented north to south like the Americas. Eurasia is east to west. Africa and the americas have wildly varying climates and environments and Eurasia is fairly similar from China to Europe.

This is from Guns,m Germs and Steel which was mostly inspired by 20th research.

Horses, chickens, horses and a long list of other tech and domesticated animals were easily transferred east to west across Eurasia.

with Africa going north to south, horses might be useful in the north but will die in the jungles and will never reach south Africa unless sent by boat. hence the transfer of knowledge and tech won't work as well as it did in Eurasia

That dig site "photograph." I keep looking for little plastic trees and a steam engine locomotive set. What is it - the camera angle? Lighting? It's a diorama, folks.

No, it’s real. I excavated at numerous rock shelters over the years, and that’s what an excavation looks like. That sheet of plywood in the center is 4’x8’ (1200x2400mm). The little table is made of 2x4 and plywood scraps. The plywood is laid down to keep the excavation walls protected

The photo was most likely scanned from an old color slide, most likely shot with Kodachrome 64–Ektachrome was rarely used because of the blue-shifted color

For anyone interested in the early humans, I highly recommend reading (or watching on Netflix) "Your Inner Fish" which goes through the archaeological record of humans and specifically gets into the 2.5-3.5myo fossils.

I'd also recommend reading "Sapiens" (which I've just started) which sheds some light on how Homo Sapien beat out Neanderthal as the dominant and now only human species.

One factor that often gets forgotten is the constant resource and talent drain that Africa has been going through since the 1500's. Up until the abolishment of slave[r]y, the healthiest and fittest portions of the population where shipped overseas.

That's not even close to true. The Atlantic and Asian Slave Trade was an abomination, but it was limited in scope to a relatively small portion of Africa (coastal West Africa and Congo). Slaves were primarily the losers of internal wars of aggression between African kingdoms, so you're starting with a subset of the survivors of the losing side of wars. (The winning side did not end up as slaves.)

The internal African slave market was vast and brutal - tens of thousands of slaves were routinely massacred in various sacrificial rituals. Like any vast system, there were "better" and "worse" slave owners, and you did not generally have hereditary slavery, but the Atlantic and Asian slave trade initially just tapped into an existing, horrifying market.

Africa is an enormous continent and the vast majority of it was unaffected by the Atlantic and Asian slave trade. Colonialism probably had a bigger total impact.

That's quite a bald-faced statement you have there. How and why is ancient DNA research "problematic and possibly wrongheaded?" We've made several interesting and important discoveries with it, (like this one), after all, so that's a pretty wild, unsupported statment...

For anyone interested in the early humans, I highly recommend reading (or watching on Netflix) "Your Inner Fish" which goes through the archaeological record of humans and specifically gets into the 2.5-3.5myo fossils.

I'd also recommend reading "Sapiens" (which I've just started) which sheds some light on how Homo Sapien beat out Neanderthal as the dominant and now only human species.

That dig site "photograph." I keep looking for little plastic trees and a steam engine locomotive set. What is it - the camera angle? Lighting? It's a diorama, folks.

Well, in the Olden Days, that is exactly how much dynamic range our cameras had. Between the bright light on the right and the shadows on the left, that's simply what a photo from 1994 _must_ look like if you want accurate colors. For art photos you could use filters, but for science, nope.

There also was no way to know how the picture came out when you took it, and both the film and the development process were expensive. Less frames, no way to know if you need to take another shot with different settings. It isn't like digital where you have a live view of the output; with an expensive camera you had a live view, but only of the input.

And to think that the genetic diversity in African populations utterly blows away the rest of humanity combined. Amazing to think of what else awaits being found.

Why is this amazing or important? If genetic diversity is so great how come there weren't very many pre-colonisation societies in Sub-Saharan Africa at the same level of development as advanced societies in Europe and Asia? You can't blame colonialism.

And to think that the genetic diversity in African populations utterly blows away the rest of humanity combined. Amazing to think of what else awaits being found.

Why is this amazing or important? If genetic diversity is so great how come there was no pre-colonisation society in Sub-Saharan Africa at the same level of development as advanced societies in Europe and Asia? You can't blame colonialism.

Umm. There were. At the time the Portuguese started exploring down the west coast if Africa in the 15th century there were a dozen or so major empires and kingdoms along the sahel and the African West Coast as far south as northern Angola, as well as all the Muslim states of North Africa, plus the East African trading states like Zanzibar and further south. There was also Ethiopia at the horn of Africa and Zimbabwe was in its decline at that stage but had been a major trading power for a couple of centuries before that.

The major advances in Europe mostly started around that era where Europe took off technologically and overtook every other major advanced civilisation on the planet with exponential expansion. But Africa was on a par with the rest of the world at the time, which is to say a mixture of highly sophisticated and technologically advanced nations and much less advanced cultures.

And to think that the genetic diversity in African populations utterly blows away the rest of humanity combined. Amazing to think of what else awaits being found.

Why is this amazing or important? If genetic diversity is so great how come there weren't very many pre-colonisation societies in Sub-Saharan Africa at the same level of development as advanced societies in v? You can't blame colonialism.

"Genetics" played no role in the development as advanced societies in Europe and Asia.

A small troupe of chimpanzees typically contains more genetic variation than all humans alive today.

There are many factors that lead to different paths and outcomes across the world...but your odd claims seem to be driven by mistaken assumptions about human socioecology and genetics.

To simplify DNA and/or genetic diversity is NOT why advanced societies arose in Europe and Asia.

And to think that the genetic diversity in African populations utterly blows away the rest of humanity combined. Amazing to think of what else awaits being found.

Scientists studying human remains in Kenya have found groups whose males were murdered by males of rival tribes then used the women as breeding stock. Many ancient Human interactions would have been what we call 'rape' today.

And to think that the genetic diversity in African populations utterly blows away the rest of humanity combined. Amazing to think of what else awaits being found.

Why is this amazing or important? If genetic diversity is so great how come there weren't very many pre-colonisation societies in Sub-Saharan Africa at the same level of development as advanced societies in Europe and Asia? You can't blame colonialism.

Geography and climate is why Africa did not produce technically sophisticated societies. In North Africa climate change forced urbanization and the river Nile provided easy communication. Sub Saharan rivers are much smaller and have significant barriers to easy navigation. Malaria is also endemic in several regions in Africa, severely limiting population growth.

And to think that the genetic diversity in African populations utterly blows away the rest of humanity combined. Amazing to think of what else awaits being found.

Why is this amazing or important? If genetic diversity is so great how come there weren't very many pre-colonisation societies in Sub-Saharan Africa at the same level of development as advanced societies in v? You can't blame colonialism.

"Genetics" played no role in the development as advanced societies in Europe and Asia.

A small troupe of chimpanzees typically contains more genetic variation than all humans alive today.

There are many factors that lead to different paths and outcomes across the world...but your odd claims seem to be driven by mistaken assumptions about human socioecology and genetics.

To simplify DNA and/or genetic diversity is NOT why advanced societies arose in Europe and Asia.

That doesn't make a whole lot of sense. Chimpanzees are irrelevant, did you know humans share 50% of their DNA with bananas? I thought you might appreciate another irrelevant fact.

The common denominator is DNA, DNA is not solely skin colour, it also helps shape our IQ and behaviour. People who evolved in inhospitable climes are more altruistic and necessarily more intelligent (having to work out ways to survive harsh winters) than people who evolved in areas where they didn't have to suffer such inclement conditions.